Mechanistic study of L-6-hydroxynicotine oxidase by DFT and ONIOM methods

L-6-Hydroxynicotine oxidase (LHNO) is a member of monoamine oxidase (MAO) family and catalyzes conversion of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during bacterial degradation of nicotine. Recent studies indicated that the enzyme catalyzes oxidation of carbon-nitrogen bond instead of previously proposed carbon-carbon bond. Based on kinetics and mutagenesis studies, Asn166, Tyr311, and Lys287 as well as an active site water molecule have roles in the catalysis of the enzyme. A number of studies including experimental and computational methods support hydride transfer mechanism in MAO family as a common mechanism in which a hydride ion transfer from amine substrate to flavin cofactor is the rate-limiting step. In this study, we formulated computational models to study the hydride transfer mechanism using crystal structure of enzyme-substrate complex. The calculations involved ONIOM and DFT methods, and we evaluated the geometry and energetics of the hydride transfer process while probing the roles of active site residues. Based on the calculations involving hydride, radical, and polar mechanisms, it was concluded that hydride transfer mechanism is the only viable mechanism for LHNO.

Molecular characterisation of Trichomonas vaginalis isolates in Southwest Turkey with multilocus sequence typing and genetic structure analysis in relation to different countries

Trichomonas vaginalis, a flagellated protozoan parasite, is among the most common sexually transmitted pathogens in the world. The present study aimed to identify the genetic profiles of T. vaginalis in the southwest of Turkey with multilocus sequence typing (MLST) and to analyse the genetic structure of the parasite in a collection of isolates from different countries. The study included 27 T. vaginalis isolates from symptomatic females in Aydin, Turkey. Seven housekeeping genes of T. vaginalis were partially amplified and sequenced after genomic DNA extraction from in vitro cultures. The allele profiles and sequence types (STs) of the isolates were determined by using the MLST database (https://pubmlst.org/tvaginalis). The genetic structure and differentiation of the parasite were analysed in relation to findings from other countries by assembling the available MLST sequences. When referred to the database, a total of 22 STs, including 18 new STs were found; besides, there were two new allele types. The genetic analysis of MLST data demonstrated the presence of two main genetic structures: Type I and Type II. In addition, the neighbor-joining method also revealed that the isolates were clustered into two groups. The genetic types distributed almost equally in the Netherlands and the USA, however, the predominance of Type I was noted in Turkey and the UK. The genetic differentiation among four countries was significant (p < .05), the gene flow was relatively high between the Netherlands and the USA, in contrast to Turkey. Finally, genetic variations were originated within populations (93.8%) rather than among populations (6.2%). In conclusion, we studied the genetic diversity of T. vaginalis isolates with MLST in the southwest of Turkey and showed the origin of genetic differentiation of the parasite among different countries. The presentation of MLST profiles and genetic variance of T. vaginalis isolates will contribute to the development of new diagnostic and treatment options for the parasite.

Relationship between the Severity of Coronary Artery Disease and Catheter-Associated Urethral Stricture in Patients with Acute Coronary Syndrome

Background: Different arterial segments throughout the vascular system develop similar grades of atherosclerosis concomitantly. Urethral ischemia has been proposed as a cause of urethral stricture. Therefore, we aimed to investigate the relationship between coronary artery disease severity using a SYNTAX score and urethral stricture occurrence after urethral catheterization in patients with non-ST-segment-elevation acute coronary syndrome (ACS). Methods: This retrospective study consisted of 306 men with urethral catheters that were diagnosed with ACS and underwent coronary angiography between January 2016 and January 2018 in Kars Kafkas University and Osmaniye Government Hospital, Turkey. Hospital records were reviewed to collect the follow-up data of the patients regarding the occurrence of urethral stricture after urethral catheterization. The study population was divided into 2 groups according to urethral stricture development, and both groups were compared statistically. Results: SYNTAX scores were significantly higher in patients with urethral stricture than in those without urethral stricture (14.86±7.11 vs. 29.25±9.79; P<0.001). The SYNTAX score (OR=1.27; 95% CI: 1.16-1.39; P<0.001), diabetes, and serum albumin were found to be the independent predictors of urethral stricture. The receiver operating characteristic curve analysis showed that the cutoff value of the SYNTAX score for urethral stricture prediction was greater than 22.5, with 76.7% sensitivity and 85.1% specificity (AUC=0.88, 95% CI: 0.84-0.91; P<0.001). Conclusion: Coronary artery disease severity graded according to the SYNTAX score is an independent predictor of urethral stricture occurrence in ACS patients with a urethral catheter inserted.

Ligand photodissociation in Ru(ii)–1,4,7-triazacyclononane complexes enhances water oxidation and enables electrochemical generation of surface active species

Ligand transformations involved in metal complexes during water oxidation (WO), such as ligand decomposition, partial oxidation, or complete dissociation have been reported, however, ligand photodissociation has not been reported yet.

Environmental pollution cost analyses of biodiesel and diesel fuels for a diesel engine

In this study, Japanese Industrial Standard diesel no 2 and waste cooking oil biodiesel fuels are compared in terms of environmental pollution cost analysis. The experiments of the diesel and biodiesel fueled diesel engine are done at 100 Nm, 200 Nm and full load (294 Nm), while engine speed is constant at 1800 rpm. The method used in this study consists of a combination of economic and environmental parameters. According to the analyses, the total environmental pollution cost of the biodiesel is higher than the diesel fuel. On the other hand, the total cost of the CO₂ emissions of the diesel fuel is generally found to be higher than biodiesel fuel in terms of the life cycle based environmental pollution cost. The specific environmental pollution cost is found as minimum at full load to be 2.217 US cent/kWh for the diesel fuel and 2.449 US cent/kWh for the biodiesel fuel at full load. On the other hand, the life cycle based specific environmental pollution cost is determined as minimum at full load to be 5.050 US cent/kWh for the diesel fuel and 5.309 US cent/kWh for the biodiesel fuel. The biodiesel fuel has higher values than diesel fuel in terms of the specific environmental pollution cost rates. The maximum total carbon dioxide emission rate is found as 0.2405 × 10^-3 kg/kJ for the biodiesel fuel at 100 Nm engine torque and the minimum one is obtained as 0.1884 × 10^-3 kg/kJ for the diesel fuel at full load. When the payback periods of the fuels are examined, biodiesel has longer period than diesel. The environmental payback period and life cycle based environmental payback period are also compared for fuels. In this context, the biodiesel has longer environmental payback periods rates than diesel. Consequently, the biodiesel fueled engine has higher environmental pollution cost rates than the diesel fueled engine, while the total carbon dioxide parameter of the diesel fuel is close to the biodiesel fuel's rate. Also, all of the other environmental parameters of diesel fuel is generally better than biodiesel. Consequently, the diesel fuel is generally better option than the biodiesel considering environmental aspects. For better environmental management, the diesel fuel utilization in the diesel engine is slightly better option than biodiesel fuel in terms of environmental pollution cost analysis.

Clinicopathological and prognostic significance of microsatellit instability (MSI) status and PDl-1 expression in Turkish patients with gastric cancer

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Background: The aim of this study was to evaluate the prognostic role of microsatellite instability (MSI) status and PD-L1 expression in surgically resected gastric cancer and the relationship of these parameters with clinicopathological features. Methods: Eighty six gastric cancer patients which had curative surgical resection at Acibadem Atakent and Maslak Hospitals between 2010 and 2017 were analysed. Tumor samples were evaluated with MSI and PD-L1 antibodies by immunohistochemical (IHC) methods. PD-L1 IHC scoring was performed using the combined positive score (CPS). Survival analysis was accomplished using the Kaplan-Meier method. Cox proportional hazard regression model was used to identify independent risk factors that affect patients' overall survival. Results: The rate of PD-L1 expression in tumor cells was 34.9% (n = 30) and the frequency of PD-L1 expression in immune cells with CPS (≥1%) was 57% (n = 49). MSI-H was detected in 11.6%(n = 10), and more observed in PD-L1 positive cases (p = 0.021). MSI-H status was significantly correlated with older age, increased tumor size, presence of PD-L1 expression, and adenocarcinoma subtype. PD-L1 expression was associated with lymph node metastasis, adenocarcinoma subtype, microsatellite instability, presence of preoperative treatment and improved response to preoperative chemotherapy. In our study, the impact of MSI status on survival was not demonstrated, but PD-L1 expression positivity(≥1%) in both tumor cells (15.7 vs 53.4 months, p = 0.008)and in immune cells (20.4 vs NR; p = 0.027) was associated with short overall survival. PD -L1 expression in tumor cells was an independent prognostic factor for overall survival in multivariate analysis (HR: 2.28, p = 0.047). Conclusions: PD-L1 expression was related to a poor prognosis in patients with gastric cancer and can represent a rational approach for PD-1/PD-L pathway-targeted immunotherapy.

Association of Serum Osmolarity With Contrast-Induced Nephropathy in Patients With ST-Segment Elevation Myocardial Infarction

Contrast-induced nephropathy (CIN) is a prevalent and serious complication after primary percutaneous coronary intervention (pPCI). Although the association between serum osmolarity and chronic kidney disease is well established, its relation to CIN in patients with ST-segment elevation myocardial infarction (STEMI) undergoing pPCI needs to be elucidated. We evaluated the predictive value of serum osmolarity for CIN development in patients with STEMI (n = 768) undergoing pPCI. Serum osmolarity on admission was calculated. The study population was divided into 2 groups according to CIN development, and both groups were compared according to clinical, laboratory, and demographic features, including the serum osmolarity. Serum osmolarity was significantly higher in patients with CIN than in those without CIN (278 [8] vs 284 [9]; P = .024). Serum osmolarity (odds ratio: 1.052; 95% confidence interval: 1.018-1.086; P = .002), hemoglobin, contrast media volume, creatinine on admission, basal SYNergy between PCI with TAXus and cardiac surgery II score, and left ventricular ejection fraction were found to be independent predictors of CIN. Serum osmolarity (given the simple calculation of this parameter on admission) can be useful to define patients with STEMI undergoing pPCI who are more likely to develop CIN.

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods

Choline oxidase catalyzes oxidation of choline into glycine betaine through a two-step reaction pathway employing flavin as the cofactor. On the light of kinetic studies, it is proposed that a hydride ion is transferred from α-carbon of choline/hydrated-betaine aldehyde to the N5 position of flavin in the rate-determining step, which is preceded by deprotonation of hydroxyl group of choline/hydrated-betaine aldehyde to one of the possible basic side chains. Using the crystal structure of glycine betaine-choline oxidase complex, we formulated two computational systems to study the hydride-transfer mechanism including main active-site amino acid side chains, flavin cofactor, and choline as a model system. The first system used pure density functional theory calculations, whereas the second approach used a hybrid ONIOM approach consisting of density functional and molecular mechanics calculations. We were able to formulate in silico model active sites to study the hydride-transfer steps by utilizing noncovalent chemical interactions between choline/betaine aldehyde and active-site amino acid chains using an atomistic approach. We evaluated and compared the geometries and energetics of hydride-transfer process using two different systems. We highlighted chemical interactions and studied the effect of protonation state of an active-site histidine base on the energetics of transfer. Furthermore, we evaluated energetics of the second hydride-transfer process as well as hydration of betaine aldehyde.

A rare cause of acute renal failure: Aortic occlusion

Aortic occlusion usually occurs in the infrarenal abdominal aorta while occlusion of the suprarenal aorta is much less common. The clinical presentation may vary from limb ischemia, neurologic symptoms of the lower extremities, abdominal symptoms, renal failure, and resistant hypertension (HTN). We present a case of suprarenal aortic occlusion presenting with renal failure and resistant HTN but without lower limb ischemia.

Adsorptive removal capacity of gravel for metal cations in the absence/presence of competitive adsorption

Locally available and low cost granular gravel as an adsorbent material was employed to determine its capacity to remove metal cations Cu(II), Fe(II), Ni(II), and Zn(II) from single metal solution and landfill leachate samples. Adsorption kinetics and mechanism under different parameters including dosage, time, and pH were studied. It was found that the experimental results fitted to the Freundlich model suggesting an adsorption process on a multilayer heterogeneous surface for both single metal solution and landfill leachate samples. The adsorption of metal cations followed second-order kinetics occurring in a single step on the surface of gravel. The order of removal efficiency of metals was found to be Cu(II)(98%) > Fe(II)(87.5%) > Zn(II)(76.05%) > Ni(II)(36.38%) in single metal solution and Cu(II)(98.3%) > Fe(II)(83%) > Zn(II)(48%) > Ni(II)(27.32%) in landfill leachate sample at pH 7. The regeneration efficiency of the metals adsorbed on the gravel resulted in the order of Fe(II)(99.54%) > Cu(II)(99%) > Ni(II)(49.46%) > Zn (II)(2.25%).

Prognostic value of preoperative neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio in patients with epithelial ovarian cancer

PURPOSE

The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) have recently been evaluated in many cancers in prediction of survival outcomes. The purpose of this study was to investigate the impact of NLR and PLR on the prognosis of patients with epithelial ovarian cancer (EOC).

MATERIALS AND METHODS

A total of 208 patients with EOC were included in the study. Hematological parameters and clinicopathological data during diagnosis were retrospectively evaluated. The cut-off values were determined by calculating receiver operating characteristic (ROC) curve analysis of the patients.

RESULTS

The median over-all survival (OS) of patients with low NLR was 69 months (95% CI, 43.0-94.9) whereas high NLR was 36 months (95% CI, 29.1-42.8). The median OS with low PLR patients was 76 months (95% CI, 46.4-105.5) and high PLR was 35 months (95% CI, 28.5-41.4). In serous tumors (70.7%), the median OS with low NLR and high NLR was 54 months (95% CI, 27.9-80.0) and 34 months (95% CI, 28.2-39.7), and for the median OS with low PLR and high PLR it was 51 months (95% CI, 2 1.2-80.7) and 35 months (95% CI, 27.8-42.1), respectively.

CONCLUSION

The present findings showed that the high NLR and high PLR were associated with poor prognosis and these values are significantly remarkable in EOC patients.